/kart

KART: Parameterization of Privacy Leakage Scenarios from Pre-trained Language Models

Primary LanguagePython

KART: Parameterization of Privacy Leakage Scenarios from Pre-trained Language Models

This is an implementation of our paper "KART: Parameterization of Privacy Leakage Scenarios from Pre-trained Language Models."

Usage

0. Requirements

  • Python 3.6.4
  • Make sure that $HOME is set to environment variable $PYTHONPATH.

1. How to make MIMIC-III-dummy-PHI

We simulate privacy leakage from clinical records using MIMIC-III-dummy-PHI.

MIMIC-III-dummy-PHI is made by embedding pieced of dummy protected health information (PHI) in MIMIC-III corpus.

1-1. Install dependencies

To install using venv module, use the following commands:

# Clone Repository
cd ~
git clone git@github.com:yutanakamura-tky/kart.git
cd ~/kart

# Install dependencies
python -m venv .venv
source .venv/bin/activate
pip install -r requirements.txt

To install using Poetry, use the following commands:

# Install Poetry
curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py > ~/get-poetry.py
cd ~
python get-poetry.py --version  1.1.4
poetry config virtualenvs.in-project true

# Clone Repository
cd ~
git clone git@github.com:yutanakamura-tky/kart.git
cd ~/kart

# Activate virtual environment & install dependencies
poetry shell
poetry install

1-2. Get Necessary files

This repository requires two datasets to create MIMIC-III-dummy-PHI:

  • MIMIC-III version 1.4 noteevents (NOTEEVENTS.csv.gz) (here)
  • n2c2 2006 De-identification challenge training dataset "Data Set 1B: De-identification Training Set" (deid_surrogate_train_all_version2.zip) (here)

Note that registration is necessary to download these datasets.

After downloading the datasets, extract them into ~/kart/corpus:

mv /path/to/NOTEEVENTS.csv.gz ~/kart/corpus
cd ~/kart/corpus
gunzip NOTEEVENTS.csv.gz

mv /path/to/deid_surrogate_train_all_version2.zip ~/kart/corpus
cd ~/kart/corpus
unzip deid_surrogate_train_all_version2.zip

1-3. Make MIMIC-III-dummy-PHI

Run make_mimic_iii_dummy_phi.sh. Make sure that you are in the virtual environment:

cd ~/kart/src
bash make_mimic_iii_dummy_phi.sh

This outputs the following files:

  • ~/kart/corpus/MIMIC_III_DUMMY_PHI_HOSPITAL.csv
  • ~/kart/corpus/MIMIC_III_DUMMY_PHI_HOSPITAL_C0P0.csv
  • ~/kart/corpus/MIMIC_III_DUMMY_PHI_HOSPITAL_C0P1.csv
  • ~/kart/corpus/MIMIC_III_DUMMY_PHI_HOSPITAL_C0P2.csv
  • ~/kart/corpus/MIMIC_III_DUMMY_PHI_HOSPITAL_C1P0.csv
  • ~/kart/corpus/MIMIC_III_DUMMY_PHI_HOSPITAL_C1P1.csv
  • ~/kart/corpus/MIMIC_III_DUMMY_PHI_HOSPITAL_C1P2.csv
  • ~/kart/corpus/MIMIC_III_DUMMY_PHI_SHADOW.csv
  • ~/kart/corpus/MIMIC_III_DUMMY_PHI_SHADOW_C0P0.csv
  • ~/kart/corpus/MIMIC_III_DUMMY_PHI_SHADOW_C0P1.csv
  • ~/kart/corpus/MIMIC_III_DUMMY_PHI_SHADOW_C0P2.csv
  • ~/kart/corpus/MIMIC_III_DUMMY_PHI_SHADOW_C1P0.csv
  • ~/kart/corpus/MIMIC_III_DUMMY_PHI_SHADOW_C1P1.csv
  • ~/kart/corpus/MIMIC_III_DUMMY_PHI_SHADOW_C1P2.csv

In our paper, we use ~/kart/corpus/MIMIC_III_DUMMY_PHI_HOSPITAL_C0P2.csv to pre-train BERT models.

We split MIMIC-III documents into two exclusive halves and name them HOSPITAL and SHADOW.

HOSPITAL_CxPy and SHADOW_CxPy are subsets of HOSPITAL and SHADOW full sets, respectively.

Pre-training BERT models with these subsets, which are smaller and less diverse than full sets, may invoke overfitting and susceptibility to privacy leakage attack.

The meaning of CxPy is:

  • C1: all 15 document categories are included.
  • C0: only two document categories "progress notes" and "discharge summary" are included.
  • P2: corpus size is limited to 100k by dropping least frequent patients.
  • P1: corpus size is limited to 10k by dropping least frequent patients.
  • P0: corpus size is limited to 1k by dropping least frequent patients.

2. How to pre-train BERT model

2-1. Convert MIMIC-III to BERT pre-training data (tfrecords format)

Run this script for two-step data conversion (CSV -> text lines -> tfrecord)

cd ~/kart/src
bash make_pretraining_data.sh

This script will output the following files:

  • ~/kart/corpus/pretraining_corpus/{half}/pretraining_corpus_{subset}_{a}.txt

    • for {half} in hospital, shadow
    • for {subset} in c0p0, c0p1, c0p2, c1p0, c1p1, c1p2
    • for {a} in hipaa, no_anonymization

  • ~/kart/corpus/pretraining_corpus/{half}/tf_examples_c0p2_{a}_128.tfrecord

  • ~/kart/corpus/pretraining_corpus/{half}/tf_examples_c0p2_{a}_128_wwm.tfrecord

    • for {half} in hospital, shadow
    • for {a} in hipaa, no_anonymization

2-2. Pre-train BERT model

To pre-train BERT model from scratch, use this command:

cd ~/kart/src
bash pretrain_bert_from_scratch.sh

To pre-train BERT model from BERT-base-uncased model, use this command:

cd ~/kart/src
# Download BERT-base-uncased model by Google Research
bash get_google_bert_model.sh
bash pretrain_bert_from_bert_base_uncased.sh

Citation

Please cite our arXiv preprint:

@misc{kart,
Author = {Yuta Nakamura and Shouhei Hanaoka and Yukihiro Nomura and Naoto Hayashi and Osamu Abe and Shuntaro Yada and Shoko Wakamiya and Eiji Aramaki},
Title = {KART: Parameterization of Privacy Leakage Scenarios from Pre-trained Language Models},
Year = {2020},
Eprint = {arXiv:2101.00036},
}